From a4145378b1c56c661ce5a6e3991b7ab84f8acad9 Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Mon, 16 Oct 2023 10:31:41 +0100 Subject: [PATCH 1/8] Addresses #2180 NTR mammary luminal epithelial cells Addresses #2180 NTR mammary luminal epithelial cells --- src/ontology/cl-edit.owl | 44 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 934a3c23d..d908f228b 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -2996,6 +2996,8 @@ Declaration(Class(obo:CL_4033053)) Declaration(Class(obo:CL_4033054)) Declaration(Class(obo:CL_4033055)) Declaration(Class(obo:CL_4033056)) +Declaration(Class(obo:CL_4033057)) +Declaration(Class(obo:CL_4033058)) Declaration(Class(obo:CL_4040000)) Declaration(Class(obo:CL_4040001)) Declaration(Class(obo:CL_4040002)) @@ -31615,6 +31617,48 @@ AnnotationAssertion(rdfs:label obo:CL_4033056 "onychocyte") SubClassOf(obo:CL_4033056 obo:CL_0000312) SubClassOf(obo:CL_4033056 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0008198)) +# Class: obo:CL_4033057 (luminal adaptive secretory precursor cell) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19648928") Annotation(oboInOwl:hasDbXref "PMID:35617956") Annotation(oboInOwl:hasDbXref "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0001-6677-8489") obo:IAO_0000115 obo:CL_4033057 "A luminal epithelial cell of the mammary gland that can proliferate and has the potential to differentiate into a lactocyte during pregnancy. In humans, a luminal adaptive secretory precursor cell can be identified by high levels of the markers EPCAM and CD49f, and in mice, it can be identified by low levels of CD29 and high levels of CD14, Kit, CD61, and TSPAN8.") +AnnotationAssertion( obo:CL_4033057 ) +AnnotationAssertion( obo:CL_4033057 ) +AnnotationAssertion( obo:CL_4033057 "2023-10-13T13:02:55Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35617956") oboInOwl:hasBroadSynonym obo:CL_4033057 "alveolar cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26390871") oboInOwl:hasBroadSynonym obo:CL_4033057 "alveolar progenitor") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2023.04.21.537845") oboInOwl:hasBroadSynonym obo:CL_4033057 "luminal progenitor") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:20346151") oboInOwl:hasBroadSynonym obo:CL_4033057 "luminal progenitor cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37380767") oboInOwl:hasBroadSynonym obo:CL_4033057 "luminal secretory cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") oboInOwl:hasExactSynonym obo:CL_4033057 "ER-negative luminal alveolar progenitor") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033057 "AP") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35617956") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033057 "AV") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0001-6677-8489") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033057 "LASP") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2023.04.21.537845") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033057 "LP") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37380767") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033057 "LumSec") +AnnotationAssertion(rdfs:label obo:CL_4033057 "luminal adaptive secretory precursor cell") +SubClassOf(obo:CL_4033057 obo:CL_0002326) + +# Class: obo:CL_4033058 (luminal hormone sensing cell) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19648928") Annotation(oboInOwl:hasDbXref "PMID:26390871") Annotation(oboInOwl:hasDbXref "PMID:34156490") Annotation(oboInOwl:hasDbXref "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0001-6677-8489") obo:IAO_0000115 obo:CL_4033058 "A luminal epithelial cell of the mammary gland that transduces endocrine cues to orchestrate proliferation, architectural remodeling, and differentiation of other cells in the mammary gland via paracrine signaling. In humans, a luminal hormone-sensing cell can be identified by high levels of EPCAM and low levels of CD49f, and in mice, it can be identified by low levels of CD29 and high levels of Foxa1, CD133, and Sca1 (Ly6a).") +AnnotationAssertion( obo:CL_4033058 ) +AnnotationAssertion( obo:CL_4033058 "https://orcid.org/0000-0003-4969-670X") +AnnotationAssertion( obo:CL_4033058 "2023-10-16T08:30:25Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") oboInOwl:hasBroadSynonym obo:CL_4033058 "ER-positive luminal hormone-sensor cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2023.04.21.537845") oboInOwl:hasBroadSynonym obo:CL_4033058 "hormone sensing cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26390871") oboInOwl:hasBroadSynonym obo:CL_4033058 "hormone-sensing mammary epithelial cell") +AnnotationAssertion(Annotation(rdfs:comment "PMID:37380767") oboInOwl:hasBroadSynonym obo:CL_4033058 "luminal hormone-responsive cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:20346151") oboInOwl:hasBroadSynonym obo:CL_4033058 "luminal mature cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2023.04.21.537845") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "HS") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26390871") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "HS-MEC") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0001-6677-8489") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "LHS") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37380767") Annotation(oboInOwl:hasRelatedSynonym obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "LumHR") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34156490") Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0003-4969-670X") rdfs:comment obo:CL_4033058 "During ductal elongation, ER activity drives expression of AREG in LHS cells, which is necessary for proliferation of the epithelium to fill the mammary fat pad.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26390871") rdfs:comment obo:CL_4033058 "Following lineage specification, a luminal hormone-sensing cell expresses receptors for one or more hormones, such as estrogens, progesterone, androgens, and prolactin.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34156490") Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0003-4969-670X") rdfs:comment obo:CL_4033058 "In response to progesterone, luminal hormone-sensing cells express TNFSF11, WNT4, and RSPO1, among other factors, which cause branching, proliferation, and partial differentiation in LASP and B-Myo cells during luteal phases of the estrous/menstrual cycle and during gestation.") +AnnotationAssertion(rdfs:label obo:CL_4033058 "luminal hormone sensing cell") +SubClassOf(obo:CL_4033058 obo:CL_0000512) +SubClassOf(obo:CL_4033058 obo:CL_0002326) + # Class: obo:CL_4040000 (glial restricted tripotential precursor cell) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:10719353") obo:IAO_0000115 obo:CL_4040000 "A glial precursor cell that generates oligodendrocytes and type-1 and type-2 astrocytes. It has been shown in some mammals that this cell type may express A2B5, nestin, FGFR-1, FGFR-2, FGFR-3, PLP, and DM-20 antigens. Unlike oligodendrocyte precursor cell, it does not initially express PDGFR-alpha and can differentiate into both type-1 and type-2 astrocytes.") From dce1251227e9a320b6b7b3b29a287839bf8d183b Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Mon, 16 Oct 2023 10:43:25 +0100 Subject: [PATCH 2/8] Fix annotation property Fix annotation property --- src/ontology/cl-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index d908f228b..4f0f9c18b 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -31646,7 +31646,7 @@ AnnotationAssertion( obo:CL_4033058 "2023-10-16T0 AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") oboInOwl:hasBroadSynonym obo:CL_4033058 "ER-positive luminal hormone-sensor cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2023.04.21.537845") oboInOwl:hasBroadSynonym obo:CL_4033058 "hormone sensing cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26390871") oboInOwl:hasBroadSynonym obo:CL_4033058 "hormone-sensing mammary epithelial cell") -AnnotationAssertion(Annotation(rdfs:comment "PMID:37380767") oboInOwl:hasBroadSynonym obo:CL_4033058 "luminal hormone-responsive cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37380767") oboInOwl:hasBroadSynonym obo:CL_4033058 "luminal hormone-responsive cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:20346151") oboInOwl:hasBroadSynonym obo:CL_4033058 "luminal mature cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2023.04.21.537845") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "HS") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26390871") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "HS-MEC") From 3fc3ba88dc8b4405bd301a4d09717830940d9088 Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Mon, 16 Oct 2023 11:10:24 +0100 Subject: [PATCH 3/8] Unify comments --- src/ontology/cl-edit.owl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 3aa32f2f9..f0e243a1b 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -31722,9 +31722,9 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2023.04.21.537845 AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26390871") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "HS-MEC") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0001-6677-8489") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "LHS") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37380767") Annotation(oboInOwl:hasRelatedSynonym obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "LumHR") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34156490") Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0003-4969-670X") rdfs:comment obo:CL_4033058 "During ductal elongation, ER activity drives expression of AREG in LHS cells, which is necessary for proliferation of the epithelium to fill the mammary fat pad.") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26390871") rdfs:comment obo:CL_4033058 "Following lineage specification, a luminal hormone-sensing cell expresses receptors for one or more hormones, such as estrogens, progesterone, androgens, and prolactin.") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34156490") Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0003-4969-670X") rdfs:comment obo:CL_4033058 "In response to progesterone, luminal hormone-sensing cells express TNFSF11, WNT4, and RSPO1, among other factors, which cause branching, proliferation, and partial differentiation in LASP and B-Myo cells during luteal phases of the estrous/menstrual cycle and during gestation.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26390871") Annotation(oboInOwl:hasDbXref "PMID:34156490") Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0003-4969-670X") rdfs:comment obo:CL_4033058 "Following lineage specification, a luminal hormone-sensing cell expresses receptors for one or more hormones, such as estrogens, progesterone, androgens, and prolactin. +In response to progesterone, luminal hormone-sensing cells express TNFSF11, WNT4, and RSPO1, among other factors, which cause branching, proliferation, and partial differentiation in LASP and B-Myo cells during luteal phases of the estrous/menstrual cycle and during gestation. +During ductal elongation, ER activity drives expression of AREG in LHS cells, which is necessary for proliferation of the epithelium to fill the mammary fat pad.") AnnotationAssertion(rdfs:label obo:CL_4033058 "luminal hormone sensing cell") SubClassOf(obo:CL_4033058 obo:CL_0000512) SubClassOf(obo:CL_4033058 obo:CL_0002326) From e50cc8b23ffe5f7497be2bb2c5f81898d28c6080 Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Mon, 16 Oct 2023 11:28:44 +0100 Subject: [PATCH 4/8] ORCID was a string --- src/ontology/cl-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index f0e243a1b..70de3ef6c 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -31711,7 +31711,7 @@ SubClassOf(obo:CL_4033057 obo:CL_0002326) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19648928") Annotation(oboInOwl:hasDbXref "PMID:26390871") Annotation(oboInOwl:hasDbXref "PMID:34156490") Annotation(oboInOwl:hasDbXref "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0001-6677-8489") obo:IAO_0000115 obo:CL_4033058 "A luminal epithelial cell of the mammary gland that transduces endocrine cues to orchestrate proliferation, architectural remodeling, and differentiation of other cells in the mammary gland via paracrine signaling. In humans, a luminal hormone-sensing cell can be identified by high levels of EPCAM and low levels of CD49f, and in mice, it can be identified by low levels of CD29 and high levels of Foxa1, CD133, and Sca1 (Ly6a).") AnnotationAssertion( obo:CL_4033058 ) -AnnotationAssertion( obo:CL_4033058 "https://orcid.org/0000-0003-4969-670X") +AnnotationAssertion( obo:CL_4033058 ) AnnotationAssertion( obo:CL_4033058 "2023-10-16T08:30:25Z"^^xsd:dateTime) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") oboInOwl:hasBroadSynonym obo:CL_4033058 "ER-positive luminal hormone-sensor cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2023.04.21.537845") oboInOwl:hasBroadSynonym obo:CL_4033058 "hormone sensing cell") From 0ee7d6ef55ebbbd8a9ce4f69c2b874bc26de8eb3 Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Mon, 16 Oct 2023 12:40:56 +0100 Subject: [PATCH 5/8] Fix change synonym type --- src/ontology/cl-edit.owl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 70de3ef6c..14f87566e 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -31721,7 +31721,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:20346151") oboInOwl:hasB AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2023.04.21.537845") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "HS") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26390871") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "HS-MEC") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0001-6677-8489") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "LHS") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37380767") Annotation(oboInOwl:hasRelatedSynonym obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "LumHR") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37380767") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "LumHR") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26390871") Annotation(oboInOwl:hasDbXref "PMID:34156490") Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0003-4969-670X") rdfs:comment obo:CL_4033058 "Following lineage specification, a luminal hormone-sensing cell expresses receptors for one or more hormones, such as estrogens, progesterone, androgens, and prolactin. In response to progesterone, luminal hormone-sensing cells express TNFSF11, WNT4, and RSPO1, among other factors, which cause branching, proliferation, and partial differentiation in LASP and B-Myo cells during luteal phases of the estrous/menstrual cycle and during gestation. During ductal elongation, ER activity drives expression of AREG in LHS cells, which is necessary for proliferation of the epithelium to fill the mammary fat pad.") From 033c99ad04ffd6f2c27f4da934c89dc7f74e86b3 Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Mon, 16 Oct 2023 14:10:52 +0100 Subject: [PATCH 6/8] Import estrogen receptor and add axioms --- src/ontology/cl-edit.owl | 3 +++ src/ontology/imports/pr_terms.txt | 3 ++- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 14f87566e..246c9a5c6 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3054,6 +3054,7 @@ Declaration(Class(obo:PR_000002123)) Declaration(Class(obo:PR_000003264)) Declaration(Class(obo:PR_000005444)) Declaration(Class(obo:PR_000005460)) +Declaration(Class(obo:PR_000007204)) Declaration(Class(obo:PR_000007785)) Declaration(Class(obo:PR_000009981)) Declaration(Class(obo:PR_000013502)) @@ -31706,6 +31707,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2023.04.21.537845 AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37380767") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033057 "LumSec") AnnotationAssertion(rdfs:label obo:CL_4033057 "luminal adaptive secretory precursor cell") SubClassOf(obo:CL_4033057 obo:CL_0002326) +SubClassOf(obo:CL_4033057 obo:CL_0011115) # Class: obo:CL_4033058 (luminal hormone sensing cell) @@ -31728,6 +31730,7 @@ During ductal elongation, ER activity drives expression of AREG in LHS cells, wh AnnotationAssertion(rdfs:label obo:CL_4033058 "luminal hormone sensing cell") SubClassOf(obo:CL_4033058 obo:CL_0000512) SubClassOf(obo:CL_4033058 obo:CL_0002326) +SubClassOf(obo:CL_4033058 ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000007204)) # Class: obo:CL_4040000 (glial restricted tripotential precursor cell) diff --git a/src/ontology/imports/pr_terms.txt b/src/ontology/imports/pr_terms.txt index bef17483a..73dca7d22 100644 --- a/src/ontology/imports/pr_terms.txt +++ b/src/ontology/imports/pr_terms.txt @@ -36,4 +36,5 @@ PR:P49582 PR:P60041 PR:Q9D387 PR:Q9Z0F7 -PR:000001666 \ No newline at end of file +PR:000001666 +PR:000007204 \ No newline at end of file From 69a27e4518e00db4e45bfaa96f96baf5effa89f2 Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Tue, 17 Oct 2023 11:44:22 +0100 Subject: [PATCH 7/8] Addresses edits requested by reviewer --- src/ontology/cl-edit.owl | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 246c9a5c6..c2b3cd07a 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -31690,7 +31690,7 @@ SubClassOf(obo:CL_4033056 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_000819 # Class: obo:CL_4033057 (luminal adaptive secretory precursor cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19648928") Annotation(oboInOwl:hasDbXref "PMID:35617956") Annotation(oboInOwl:hasDbXref "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0001-6677-8489") obo:IAO_0000115 obo:CL_4033057 "A luminal epithelial cell of the mammary gland that can proliferate and has the potential to differentiate into a lactocyte during pregnancy. In humans, a luminal adaptive secretory precursor cell can be identified by high levels of the markers EPCAM and CD49f, and in mice, it can be identified by low levels of CD29 and high levels of CD14, Kit, CD61, and TSPAN8.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19648928") Annotation(oboInOwl:hasDbXref "PMID:35617956") Annotation(oboInOwl:hasDbXref "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0001-6677-8489") obo:IAO_0000115 obo:CL_4033057 "A luminal epithelial cell of the mammary gland that can proliferate and has the potential to differentiate into a lactocyte during pregnancy. In humans, a luminal adaptive secretory precursor cell can be identified by high levels of the markers EpCAM and CD49f, and in mice it can be identified by low levels of CD29 and high levels of CD14, Kit, CD61, and Tspan8.") AnnotationAssertion( obo:CL_4033057 ) AnnotationAssertion( obo:CL_4033057 ) AnnotationAssertion( obo:CL_4033057 "2023-10-13T13:02:55Z"^^xsd:dateTime) @@ -31709,25 +31709,23 @@ AnnotationAssertion(rdfs:label obo:CL_4033057 "luminal adaptive secretory precur SubClassOf(obo:CL_4033057 obo:CL_0002326) SubClassOf(obo:CL_4033057 obo:CL_0011115) -# Class: obo:CL_4033058 (luminal hormone sensing cell) +# Class: obo:CL_4033058 (luminal hormone-sensing cell) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19648928") Annotation(oboInOwl:hasDbXref "PMID:26390871") Annotation(oboInOwl:hasDbXref "PMID:34156490") Annotation(oboInOwl:hasDbXref "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0001-6677-8489") obo:IAO_0000115 obo:CL_4033058 "A luminal epithelial cell of the mammary gland that transduces endocrine cues to orchestrate proliferation, architectural remodeling, and differentiation of other cells in the mammary gland via paracrine signaling. In humans, a luminal hormone-sensing cell can be identified by high levels of EPCAM and low levels of CD49f, and in mice, it can be identified by low levels of CD29 and high levels of Foxa1, CD133, and Sca1 (Ly6a).") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19648928") Annotation(oboInOwl:hasDbXref "PMID:26390871") Annotation(oboInOwl:hasDbXref "PMID:34156490") Annotation(oboInOwl:hasDbXref "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0001-6677-8489") obo:IAO_0000115 obo:CL_4033058 "A luminal epithelial cell of the mammary gland that transduces endocrine cues to orchestrate proliferation, architectural remodeling, and differentiation of other cells in the mammary gland via paracrine signaling. This cell expresses high levels of estrogen receptors. In humans, a luminal hormone-sensing cell can be identified by high levels of EpCAM and low levels of CD49f, and in mice it can be identified by low levels of CD29 and high levels of Foxa1, CD133, and Sca1 (Ly6a).") AnnotationAssertion( obo:CL_4033058 ) AnnotationAssertion( obo:CL_4033058 ) AnnotationAssertion( obo:CL_4033058 "2023-10-16T08:30:25Z"^^xsd:dateTime) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") oboInOwl:hasBroadSynonym obo:CL_4033058 "ER-positive luminal hormone-sensor cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2023.04.21.537845") oboInOwl:hasBroadSynonym obo:CL_4033058 "hormone sensing cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26390871") oboInOwl:hasBroadSynonym obo:CL_4033058 "hormone-sensing mammary epithelial cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37380767") oboInOwl:hasBroadSynonym obo:CL_4033058 "luminal hormone-responsive cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:20346151") oboInOwl:hasBroadSynonym obo:CL_4033058 "luminal mature cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") oboInOwl:hasExactSynonym obo:CL_4033058 "ER-positive luminal hormone-sensor cell") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2023.04.21.537845") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "HS") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26390871") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "HS-MEC") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0001-6677-8489") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "LHS") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37380767") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "LumHR") -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26390871") Annotation(oboInOwl:hasDbXref "PMID:34156490") Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0003-4969-670X") rdfs:comment obo:CL_4033058 "Following lineage specification, a luminal hormone-sensing cell expresses receptors for one or more hormones, such as estrogens, progesterone, androgens, and prolactin. -In response to progesterone, luminal hormone-sensing cells express TNFSF11, WNT4, and RSPO1, among other factors, which cause branching, proliferation, and partial differentiation in LASP and B-Myo cells during luteal phases of the estrous/menstrual cycle and during gestation. -During ductal elongation, ER activity drives expression of AREG in LHS cells, which is necessary for proliferation of the epithelium to fill the mammary fat pad.") -AnnotationAssertion(rdfs:label obo:CL_4033058 "luminal hormone sensing cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26390871") Annotation(oboInOwl:hasDbXref "PMID:34156490") Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0003-4969-670X") rdfs:comment obo:CL_4033058 "Following lineage specification, a luminal hormone-sensing cell expresses receptors for one or more hormones, such as estrogens, progesterone, androgens, and prolactin. In response to progesterone, luminal hormone-sensing cells express TNFSF11, WNT4, and RSPO1, among other factors, which cause branching, proliferation, and partial differentiation in LASP and B-Myo cells during luteal phases of the estrous/menstrual cycle and during gestation. During ductal elongation, ER activity drives expression of AREG in LHS cells, which is necessary for proliferation of the epithelium to fill the mammary fat pad.") +AnnotationAssertion(rdfs:label obo:CL_4033058 "luminal hormone-sensing cell") SubClassOf(obo:CL_4033058 obo:CL_0000512) SubClassOf(obo:CL_4033058 obo:CL_0002326) SubClassOf(obo:CL_4033058 ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000007204)) From 045eeaec90c34c05c48887d345a599ab73db3745 Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Tue, 17 Oct 2023 13:56:03 +0100 Subject: [PATCH 8/8] Add " of mammary gland" to the labels --- src/ontology/cl-edit.owl | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 0cce3d2e5..7537ca29e 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -31701,7 +31701,7 @@ AnnotationAssertion(rdfs:label obo:CL_4033056 "onychocyte") SubClassOf(obo:CL_4033056 obo:CL_0000312) SubClassOf(obo:CL_4033056 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0008198)) -# Class: obo:CL_4033057 (luminal adaptive secretory precursor cell) +# Class: obo:CL_4033057 (luminal adaptive secretory precursor cell of mammary gland) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19648928") Annotation(oboInOwl:hasDbXref "PMID:35617956") Annotation(oboInOwl:hasDbXref "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0001-6677-8489") obo:IAO_0000115 obo:CL_4033057 "A luminal epithelial cell of the mammary gland that can proliferate and has the potential to differentiate into a lactocyte during pregnancy. In humans, a luminal adaptive secretory precursor cell can be identified by high levels of the markers EpCAM and CD49f, and in mice it can be identified by low levels of CD29 and high levels of CD14, Kit, CD61, and Tspan8.") AnnotationAssertion( obo:CL_4033057 ) @@ -31718,11 +31718,11 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:35617956") Annotation(ob AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0001-6677-8489") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033057 "LASP") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "doi:10.1101/2023.04.21.537845") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033057 "LP") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37380767") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033057 "LumSec") -AnnotationAssertion(rdfs:label obo:CL_4033057 "luminal adaptive secretory precursor cell") +AnnotationAssertion(rdfs:label obo:CL_4033057 "luminal adaptive secretory precursor cell of mammary gland") SubClassOf(obo:CL_4033057 obo:CL_0002326) SubClassOf(obo:CL_4033057 obo:CL_0011115) -# Class: obo:CL_4033058 (luminal hormone-sensing cell) +# Class: obo:CL_4033058 (luminal hormone-sensing cell of mammary gland) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:19648928") Annotation(oboInOwl:hasDbXref "PMID:26390871") Annotation(oboInOwl:hasDbXref "PMID:34156490") Annotation(oboInOwl:hasDbXref "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0001-6677-8489") obo:IAO_0000115 obo:CL_4033058 "A luminal epithelial cell of the mammary gland that transduces endocrine cues to orchestrate proliferation, architectural remodeling, and differentiation of other cells in the mammary gland via paracrine signaling. This cell expresses high levels of estrogen receptors. In humans, a luminal hormone-sensing cell can be identified by high levels of EpCAM and low levels of CD49f, and in mice it can be identified by low levels of CD29 and high levels of Foxa1, CD133, and Sca1 (Ly6a).") AnnotationAssertion( obo:CL_4033058 ) @@ -31738,7 +31738,7 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26390871") Annotation(ob AnnotationAssertion(Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0001-6677-8489") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "LHS") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37380767") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4033058 "LumHR") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:26390871") Annotation(oboInOwl:hasDbXref "PMID:34156490") Annotation(oboInOwl:hasDbXref "https://orcid.org/0000-0003-4969-670X") rdfs:comment obo:CL_4033058 "Following lineage specification, a luminal hormone-sensing cell expresses receptors for one or more hormones, such as estrogens, progesterone, androgens, and prolactin. In response to progesterone, luminal hormone-sensing cells express TNFSF11, WNT4, and RSPO1, among other factors, which cause branching, proliferation, and partial differentiation in LASP and B-Myo cells during luteal phases of the estrous/menstrual cycle and during gestation. During ductal elongation, ER activity drives expression of AREG in LHS cells, which is necessary for proliferation of the epithelium to fill the mammary fat pad.") -AnnotationAssertion(rdfs:label obo:CL_4033058 "luminal hormone-sensing cell") +AnnotationAssertion(rdfs:label obo:CL_4033058 "luminal hormone-sensing cell of mammary gland") SubClassOf(obo:CL_4033058 obo:CL_0000512) SubClassOf(obo:CL_4033058 obo:CL_0002326) SubClassOf(obo:CL_4033058 ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000007204))